It quotes staff as encouraging Safiya Ghori-Ahmad, during her short period working at the commission, to call in sick on the days that particular commissioners were in the office, to “downplay her religious affiliation” and to emphasize that she is a “mainstream and ‘moderate’ Muslim” who doesn’t cover her hair.

The lawsuit, which follows an Equal Employment Opportunity Commission complaint that Ghori-Ahmad filed in 2010, lays blame on several longtime commissioners, including Nina Shea, an attorney and writer who focuses on religious freedom crises abroad, particularly the plight of Christian minorities. The suit quotes Shea as writing that “hiring a Muslim like Ms. Ghori-Ahmad to analyze religious freedom in Pakistan would be like ‘hiring an IRA activist to research the UK twenty years ago.’”

The commission referred questions to the Justice Department, which represents the quasi-governmental organization; Justice officials declined to immediately comment.

Shea and several other commissioners have long been accused of criticizing aspects of the Islamic faith in a way that unfairly stigmatizes all Muslims. Others see Shea and her arguments as a bold challenge to Islamic extremism and terrorism.

The suit quotes the commission’s policy and research director, Knox Thames, as telling Ghori-Ahmad that the offer to be a South Asia policy analyst was retracted — weeks after being made, and after she had quit her other job — because “certain Commissioners objected to her Muslim faith and affiliation … He said he was sorry this had happened,” the suit says.

Also accused of leading the alleged discrimination was longtime commission chairman Leonard Leo, a key consultant at times to Republican leaders on Catholic issues and executive vice president of the Federalist Society.

Its budget was ultimately cut by a quarter and long-serving commissioners were forced out by retroactive term limits.

UPDATE, 6:05 p.m. Monday:

On Monday, Shea e-mailed the Washington Post to say that she is unfairly being depicted as bigoted that she and opposed hiring Ghori-Ahmad because of the lawyer’s views, including her analysis of the causes of the 2008 terrorist attacks in Mumbai, India.

“Her writings reflect [the Muslim American Public Affairs Council] activism and bias, not scholarship, which would not serve us well on the research staff,” Shea’s e-mail Monday said.

Shea noted work she has done in support of some Muslim minority groups, including Uighurs in China and the Ahmadiyya. She also noted that the former president of Indonesia, a Muslim, wrote the forward of a book she wrote in 2011 about the dangers of anti-blasphemy laws in Muslim communities.